lines 3-5 were there because I was attempting to initialize the array the same way I had for my 2-d arrays later on. ( I guessed that strings were just char arrays and would need similar initialization)

After removing the * as suggested I just get seg faults.
I realize that segfault is a bit more difficult to diagnose
if i comment out just the assignment line it works fine (line 18)

I don't see anything related to this in my messages
icc -Wall rotation.cpp only shows messages from later in the code

An std::string is based on a char array, but they are not equivalent datatypes.

string *name; //creates a pointer to an std::string
name = new string[atoms]; //expands the pointer to an array of (atoms) pointers to strings
for (int i=0;i<atoms;i++){
name[i]=new string[8];
//you are trying to create a new array dimension that contains an incompatible type
//you need to assign literals to the dereferenced pointer(s)
//i.e. (*arrayName[element]) = "a literal"
}